Manganese in PDB 6f4r: Human JMJD5 (N308C) in Complex with Mn(II), Nog and RCCD1 (139-143) (Complex-3)

All present enzymatic activity of Human JMJD5 (N308C) in Complex with Mn(II), Nog and RCCD1 (139-143) (Complex-3):
1.14.11.47;

The structure of Human JMJD5 (N308C) in Complex with Mn(II), Nog and RCCD1 (139-143) (Complex-3), PDB code: 6f4r was solved by R.Chowdhury, M.S.Islam, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.84 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.429, 64.810, 77.982, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 16.2

The binding sites of Manganese atom in the Human JMJD5 (N308C) in Complex with Mn(II), Nog and RCCD1 (139-143) (Complex-3) (pdb code 6f4r). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Human JMJD5 (N308C) in Complex with Mn(II), Nog and RCCD1 (139-143) (Complex-3), PDB code: 6f4r:

Manganese binding site 1 out of 1 in the Human JMJD5 (N308C) in Complex with Mn(II), Nog and RCCD1 (139-143) (Complex-3)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human JMJD5 (N308C) in Complex with Mn(II), Nog and RCCD1 (139-143) (Complex-3) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:11.5 occ:1.00 OD2 A:ASP323 2.1 13.4 1.0 O2 A:OGA502 2.2 13.4 1.0 O2' A:OGA502 2.2 12.9 1.0 NE2 A:HIS321 2.2 12.1 1.0 O A:HOH749 2.3 15.2 1.0 NE2 A:HIS400 2.3 11.7 1.0 C1 A:OGA502 2.9 13.6 1.0 C2 A:OGA502 2.9 12.2 1.0 CG A:ASP323 3.1 13.9 1.0 CE1 A:HIS321 3.1 11.9 1.0 CE1 A:HIS400 3.2 11.5 1.0 HE1 A:HIS321 3.2 14.2 1.0 CD2 A:HIS321 3.3 11.5 1.0 HE1 A:HIS400 3.3 13.8 1.0 CD2 A:HIS400 3.3 11.5 1.0 OD1 A:ASP323 3.4 15.7 1.0 HD2 A:HIS321 3.5 13.8 1.0 HD2 A:HIS400 3.5 13.8 1.0 HZ2 A:TRP414 3.6 24.0 0.6 O A:HOH728 3.9 17.4 1.0 HZ2 A:TRP414 3.9 29.8 0.4 HD2 B:ARG141 3.9 35.2 0.6 HB2 B:ARG141 4.1 33.3 0.6 O1 A:OGA502 4.2 14.8 1.0 HB3 B:ARG141 4.2 33.3 0.6 O A:HOH731 4.2 19.0 0.4 N1 A:OGA502 4.2 12.8 1.0 HE1 A:TRP414 4.2 20.8 0.4 ND1 A:HIS321 4.3 12.3 1.0 HD22 A:ASN327 4.3 16.5 1.0 HE1 A:TRP414 4.3 21.5 0.6 ND1 A:HIS400 4.3 12.1 1.0 CG A:HIS321 4.4 11.5 1.0 HH2 A:TRP310 4.4 20.3 1.0 CG A:HIS400 4.5 11.0 1.0 CZ2 A:TRP414 4.5 20.1 0.6 CB A:ASP323 4.5 13.1 1.0 HB2 A:ASP323 4.5 15.7 1.0 CB B:ARG141 4.6 27.8 0.6 HD3 B:ARG141 4.6 35.2 0.6 CZ2 A:TRP414 4.7 24.8 0.4 HZ2 A:TRP310 4.7 20.2 1.0 CD B:ARG141 4.7 29.4 0.6 HD21 A:ASN327 4.8 16.5 1.0 H4C2 A:OGA502 4.8 15.7 1.0 O A:HOH615 4.8 49.2 1.0 NE1 A:TRP414 4.9 17.4 0.4 H4C1 A:OGA502 4.9 15.7 1.0 ND2 A:ASN327 4.9 13.7 1.0 CH2 A:TRP310 4.9 16.9 1.0 H1 A:OGA502 4.9 15.3 1.0 C4 A:OGA502 4.9 13.1 1.0 O B:CYS139 4.9 27.4 0.6 HB3 A:ASP323 5.0 15.7 1.0 NE1 A:TRP414 5.0 17.9 0.6

S.E.Wilkins, S.Islam, J.M.Gannon, S.Markolovic, R.J.Hopkinson, W.Ge, C.J.Schofield, R.Chowdhury. JMJD5 Is A Human Arginyl C-3 Hydroxylase. Nat Commun V. 9 1180 2018.
ISSN: ESSN 2041-1723
PubMed: 29563586
DOI: 10.1038/S41467-018-03410-W